sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 1.000 | |
| 3to0 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.594 | |
| 4ttb | FMN | Iodotyrosine deiodinase 1 | / | 0.592 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.567 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.525 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.489 | |
| 4i4b | 1CV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.489 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.480 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.479 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.478 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.477 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.475 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.475 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.475 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.472 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.470 | |
| 4a5l | NDP | Thioredoxin reductase | / | 0.469 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.468 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.468 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.467 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.466 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.465 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.464 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.463 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.463 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.461 | |
| 3pxv | FMN | Nitroreductase | / | 0.461 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.461 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 2q0k | NAP | Thioredoxin reductase | 1.8.1.9 | 0.459 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.458 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.457 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.457 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.457 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.456 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.455 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.455 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.454 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.454 | |
| 4blr | UTP | NTPase P4 | / | 0.454 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.454 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.453 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.453 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.453 | |
| 3sc1 | 3S1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.453 | |
| 1kqb | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.452 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.452 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.452 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.452 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1bp6 | UMP | Thymidylate synthase | / | 0.451 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.451 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.451 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.451 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.450 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.450 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.450 | |
| 4hdh | ATP | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.449 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.449 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.448 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.448 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.448 | |
| 3ntd | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.448 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.448 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.447 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.447 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.447 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.447 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.446 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 3ieu | GDP | GTPase Era | / | 0.446 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4bqw | QNM | Egl nine homolog 1 | / | 0.446 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.445 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.445 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.445 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 1c7o | PPG | Hemolysin | / | 0.444 | |
| 1kny | APC | Kanamycin nucleotidyltransferase | 2.7.7 | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2wtk | ANP | STE20-related kinase adapter protein alpha | / | 0.444 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.444 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.444 | |
| 4tl8 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.443 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.443 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.443 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1j36 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.442 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3x2w | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.442 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.442 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.441 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.441 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.441 | |
| 1w4a | APC | NTPase P4 | / | 0.441 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.441 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.441 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3mje | NDP | AmphB | / | 0.441 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.441 | |
| 4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.440 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.440 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.440 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.440 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.440 |